Diffusion plays an important role in Earth sciences to estimate the timescales of geological processes such as erosion, sediment burial, and magma cooling. In igneous systems, these diffusive processes are recorded in the form of crystal zoning. However, meaningful interpretation of these signatures is often hampered by the fact that they cannot be unambiguously ascribed to a single process (e.g., magmatic fractionation, diffusion limited transport in the crystal or in the liquid). Here we show that Mg and Fe isotope fractionations in olivine crystals can be used to trace diffusive processes in magmatic systems. Over sixty olivine fragments from Hawaiian basalts show isotopically fractionated Mg and Fe relative to basalts worldwide, with up to 0.4‰ variation in ²⁶Mg/²⁴Mg ratios and 1.6‰ variation in ⁵⁶Fe/⁵⁴Fe ratios. The linearly and negatively correlated Mg and Fe isotopic compositions [i.e., δ⁵⁶Fe = (− 3.3 ± 0.3) × δ²⁶Mg], co-variations of Mg and Fe isotopic compositions with Fe/Mg ratios of olivine fragments, and modeling results based on Mg and Fe elemental profiles demonstrate the coupled Mg and Fe isotope fractionation to be a manifestation of Mg–Fe inter-diffusion in zoned olivines during magmatic differentiation. This characteristic can be used to constrain the nature of mineral zoning in igneous and metamorphic rocks, and hence determine the residence times of crystals in magmas, the composition of primary melts, and the duration of metamorphic events. With improvements in methodology, in situ isotope mapping will become an essential tool of petrology to identify diffusion in crystals.